Man pages for erflynn/exprsex
Rank-Based Sex Labeling of Microarray Expression Data
| dot-check_entrez_overlap | Count the length of overlap with entrez ids for a sequence of... |
| dot-checkExprMatFormat | Checks that an input expression matrix has the correct format |
| dot-checkFitFormat | Checks that a fit object has the correct structure |
| dot-checkGeneFormat | Checks that the expression matrix rownames contain the genes... |
| dot-checkMatching | Checks that sex labels and expression matrix match |
| dot-checkProbeMapping | Checks that a probe mapping has the correct format. |
| dot-checkSexLabFormat | Checks that input sex labels have the correct format |
| dot-checkTrainInputFormat | Checks that expression matrix and sex labels have the correct... |
| dot-clean_mapping | Clean up the mapping output |
| dot-convertGenes | Convert the expression matrix to genes. This takes the... |
| dot-detect_ensembl_cols | Identify the ensembl columns and return the one with the max... |
| dot-detect_entrez_ids_name | Looks for entrez ids by trying to find a column name named... |
| dot-detect_genbank_cols | Identify the genbank columns and return the first (Note -... |
| dot-detect_genbank_cols_name | Looks for genbank cols by trying to find a column name named... |
| dot-detect_hgnc_cols | Identify the HGNC columns and return the first (Note - this... |
| dot-detect_int_cols | Identify integer only only columns, hopefully these are... |
| dot-detect_refseq_cols | Identify the refseq columns and return the one with the most... |
| dot-detect_unigene_cols | Identify the unigene columns and return the one with the most... |
| dot-expDataToRanks | Convert an expression dataset to ranks. |
| dot-extract_biomart_ref | Extract a gene mapping table from biomaRt, this contains... |
| dot-extract_entrez | Gets a list of all entrez ids for an organism. This pulls the... |
| dot-filterGenesByVar | Helper function to filter genes based on their standard... |
| dot-find_col_loc | Heper function to find the location within a column of an ID.... |
| dot-find_entrez_w_in_block | Identify columns that might have entrez in them. This would... |
| dot-geomMeanAcrossGenes | Helper function to calculate geometric mean of a set of genes... |
| dot-geomMeanScore | Calculate the score geometric mean of male genes - female... |
| dot-get_genbank | Gets a mapping of genbank to entrez. Note - these tables are... |
| dot-get_ref_data | Generate the desired mapping data for that organism |
| dot-get_unigene | Gets a mapping of unigene ids to entrez ids. This pulls the... |
| dot-get_xy_genes | Gets a table of all the X,Y genes for that organism with the... |
| dot-load_ref | Load the desired reference data mapping table. The reference... |
| dot-map_from_ensembl | Helper function to extract and map ensembl to entrez |
| dot-map_from_genbank | Helper function to extract and map genbank to entrez |
| dot-map_from_hgnc | Helper function to extract and map HGNC to entrez Note - this... |
| dot-map_from_refseq | Helper function to extract and map refseq to entrez |
| dot-map_from_unigene | Helper function to extract and map unigene to entrez |
| dot-my_assert | Custom assertion function, prints formatted error messages... |
| dot-parse_multi_col | Helper function to parse a pattern out of a multi-column.... |
| dot-predDf | Helper function to generate a predicted probability df for a... |
| dot-reform_entrez_df | Helper function to reformat entrez gene/probe data frame.... |
| dot-reorderGeneMat | Reorder the expression matrix so it contains the... |
| exprsex | exprsex: A package for sex labeling microarray expression... |
| generate_all_ref | Code to generate all reference tables for rat, mouse, and... |
| getConsensusGenes | Create a consensus gene list from a set of expression... |
| getPrepGSE | Get and prepare a gse file for sex labeling by converting it... |
| map_mult_gpl | Wrapper to parse and map data from multiple gpls. |
| parse_entrez_from_gpl | Parse and map entrez data from a GPL annotation. |
| predProba | Return the predicted probabilities and sex labels for an... |
| predSexLab | Use a particular sex labeling fit to label an input dataset |
| prepFromExpr | Prepare data from an existing expression matrix |
| reorderRank | Reorder and rank a gene expression matrix. We then use this... |
| runSexLab | Run sex labeling using default settings. |
| sex_lab_genes | Default genes used for sex labeling. |
| trainProba | Fit a logistic curve to the sex labeling fit so that we can... |
| trainSexLab | Train a sex labeling classifier using input training data. |
